scholarly journals Adaptive introgression underlies polymorphic seasonal camouflage in snowshoe hares

Science ◽  
2018 ◽  
Vol 360 (6395) ◽  
pp. 1355-1358 ◽  
Author(s):  
Matthew R. Jones ◽  
L. Scott Mills ◽  
Paulo Célio Alves ◽  
Colin M. Callahan ◽  
Joel M. Alves ◽  
...  
Keyword(s):  
Genetic Variants ◽  
High Frequency ◽  
Coat Color ◽  
Ecological Traits ◽  
Interspecific Gene Flow ◽  
Mild Winter ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Snowshoe Hares ◽  
History Of

Snowshoe hares (Lepus americanus) maintain seasonal camouflage by molting to a white winter coat, but some hares remain brown during the winter in regions with low snow cover. We show that cis-regulatory variation controlling seasonal expression of the Agouti gene underlies this adaptive winter camouflage polymorphism. Genetic variation at Agouti clustered by winter coat color across multiple hare and jackrabbit species, revealing a history of recurrent interspecific gene flow. Brown winter coats in snowshoe hares likely originated from an introgressed black-tailed jackrabbit allele that has swept to high frequency in mild winter environments. These discoveries show that introgression of genetic variants that underlie key ecological traits can seed past and ongoing adaptation to rapidly changing environments.

Prevalence and Adaptive Impact of Introgression

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nathaniel B. Edelman ◽  
James Mallet
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Genetic Variants ◽  
Genomic Data ◽  
Annual Review ◽  
Publication Date ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals PathFinder: Bayesian inference of clone migration histories in cancer

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i675-i683
Author(s):  
Sudhir Kumar ◽  
Antonia Chroni ◽  
Koichiro Tamura ◽  
Maxwell Sanderford ◽  
Olumide Oladeinde ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Cancer Cells ◽  
Bayesian Approach ◽  
Genetic Variants ◽  
Cancer Development ◽  
Posterior Probabilities ◽  
Migration Routes ◽  
Primary Tumors ◽  
History Of ◽  
The Web

Abstract Summary Metastases cause a vast majority of cancer morbidity and mortality. Metastatic clones are formed by dispersal of cancer cells to secondary tissues, and are not medically detected or visible until later stages of cancer development. Clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here, we present a new Bayesian approach, PathFinder, for reconstructing the routes of cancer cell migrations. PathFinder uses the clone phylogeny, the number of mutational differences among clones, and the information on the presence and absence of observed clones in primary and metastatic tumors. By analyzing simulated datasets, we found that PathFinder performes well in reconstructing clone migrations from the primary tumor to new metastases as well as between metastases. It was more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor, and by increasing the number of genetic variants assayed per clone. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes. In conclusion, we anticipate that the use of PathFinder will enable a more reliable inference of migration histories and their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases. Availability and implementation PathFinder is available on the web at https://github.com/SayakaMiura/PathFinder.

scholarly journals Molecular Signatures of Reticulate Evolution within the Complex of European Pine Taxa

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 489
Author(s):  
Bartosz Łabiszak ◽  
Witold Wachowiak
Keyword(s):  
Gene Flow ◽  
Reticulate Evolution ◽  
Modeling Framework ◽  
Closely Related Species ◽  
Interspecific Gene Flow ◽  
Nucleotide Sequence Variation ◽  
History Of ◽  
Best Fitting ◽  
Species Integrity

Speciation mechanisms, including the role of interspecific gene flow and introgression in the emergence of new species, are the major focus of evolutionary studies. Inference of taxonomic relationship between closely related species may be challenged by past hybridization events, but at the same time, it may provide new knowledge about mechanisms responsible for the maintenance of species integrity despite interspecific gene flow. Here, using nucleotide sequence variation and utilizing a coalescent modeling framework, we tested the role of hybridization and introgression in the evolutionary history of closely related pine taxa from the Pinus mugo complex and P. sylvestris. We compared the patterns of polymorphism and divergence between taxa and found a great overlap of neutral variation within the P. mugo complex. Our phylogeny reconstruction indicated multiple instances of reticulation events in the past, suggesting an important role of interspecific gene flow in the species divergence. The best-fitting model revealed P. mugo and P. uncinata as sister species with basal P. uliginosa and asymmetric migration between all investigated species after their divergence. The magnitude of interspecies gene flow differed greatly, and it was consistently stronger from representatives of P. mugo complex to P. sylvestris than in the opposite direction. The results indicate the prominent role of reticulation evolution in those forest trees and provide a genetic framework to study species integrity maintained by selection and local adaptation.

scholarly journals Gaining Insights in Loading Events for Wind Turbine Drivetrain Prognostics

2020 ◽  
Author(s):  
Pieter-Jan Daems ◽  
Y. Guo ◽  
S. Sheng ◽  
C. Peeters ◽  
P. Guillaume ◽  
...  
Keyword(s):  
High Frequency ◽  
Failure Modes ◽  
Measurement Data ◽  
Wind Farms ◽  
Frequency Measurement ◽  
Operating Conditions ◽  
Failure Data ◽  
The World ◽  
Operations And Maintenance ◽  
History Of

Abstract Wind energy is one of the largest sources of renewable energy in the world. To further reduce the operations and maintenance (O&M) costs of wind farms, it is essential to be able to accurately pinpoint the root causes of different failure modes of interest. An example of such a failure mode that is not yet fully understood is white etching cracks (WEC). This can cause the bearing lifetime to be reduced to 5–10% of its design value. Multiple hypotheses are available in literature concerning its cause. To be able to validate or disprove these hypotheses, it is essential to have historic high-frequency measurement data (e.g., load and vibration levels) available. In time, this will allow linking to the history of the turbine operating data with failure data. This paper discusses the dynamic loading on the turbine during certain events (e.g., emergency stops, run-ups, and during normal operating conditions). By combining the number of specific events that each turbine has seen with the severity of each event, it becomes possible to assess which turbines are most likely to show signs of damage.

scholarly journals Helicobacter pylori infection and its correlates among the patients of peptic perforation and gastric carcinoma

2020 ◽  
Vol 7 (5) ◽  
pp. 1518
Author(s):  
Subhendu Bikas Saha ◽  
Sabyasachi Bakshi ◽  
Tapas Mandal
Keyword(s):  
Gastric Carcinoma ◽  
High Frequency ◽  
Age Group ◽  
Morbid Condition ◽  
Exclusion Criteria ◽  
Chronic Alcoholic ◽  
Female Ratio ◽  
History Of ◽  
Study Population ◽  
H Pylori

Background: Presence of H. pylori infection was found associated with peptic perforation and gastric carcinoma. Present study tried to estimate the prevalence of H. pylori infection in those patients and to find out the correlates of H. pylori infection.Methods: After matching the inclusion and exclusion criteria, all cases of diagnosed peptic perforation and gastric carcinoma were taken for this prospective, single center, observational study.Results: Among the study population, gastric carcinoma was found in higher age group; whereas peptic perforation was found in lower age group; male and female ratio was 2:1 in both groups of patient. Laborer and housewives were mostly affected in both cases. Gastric carcinoma was more prevalent in urban residents, opposite was seen in peptic perforation. Most patients in two groups had no previous co-morbid condition. Use of NSAIDs was found in high frequency in both groups. Most of the patients were chronic alcoholic and chronic smoker, and most of them had history of taking spicy foods more than twice in a week.Conclusions: H. pylori infection was found in high frequency in both group of patients, and it was higher in peptic perforation. The study establishes the association of H. pylori with the gastric carcinoma and peptic perforation.

scholarly journals Adaptation and competition in deteriorating environments

2021 ◽  
Vol 288 (1946) ◽  
pp. 20202967
Author(s):  
Romana Limberger ◽  
Gregor F. Fussmann
Keyword(s):  
Salt Stress ◽  
Experimental Evolution ◽  
Competitive Ability ◽  
High Salt ◽  
Competitive Interactions ◽  
Complex Interplay ◽  
Population Growth Rates ◽  
Changing Environments ◽  
History Of

Evolution might rescue populations from extinction in changing environments. Using experimental evolution with microalgae, we investigated if competition influences adaptation to an abiotic stressor, and vice versa, if adaptation to abiotic change influences competition. In a first set of experiments, we propagated monocultures of five species with and without increasing salt stress for approximately 180 generations. When assayed in monoculture, two of the five species showed signatures of adaptation, that is, lines with a history of salt stress had higher population growth rates at high salt than lines without prior exposure to salt. When assayed in mixtures of species, however, only one of these two species had increased population size at high salt, indicating that competition can alter how adaptation to abiotic change influences population dynamics. In a second experiment, we cultivated two species in monocultures and in pairs, with and without increasing salt. While we found no effect of competition on adaptation to salt, our experiment revealed that evolutionary responses to salt can influence competition. Specifically, one of the two species had reduced competitive ability in the no-salt environment after long-term exposure to salt stress. Collectively, our results highlight the complex interplay of adaptation to abiotic change and competitive interactions.

scholarly journals Balancing selection and introgression of newt immune-response genes

2018 ◽  
Vol 285 (1884) ◽  
pp. 20180819 ◽  
Author(s):  
Anna Fijarczyk ◽  
Katarzyna Dudek ◽  
Marta Niedzicka ◽  
Wiesław Babik
Keyword(s):  
Gene Flow ◽  
Genetic Variants ◽  
Balancing Selection ◽  
Species Boundaries ◽  
Adaptive Introgression ◽  
Interspecific Introgression ◽  
Differential Gene ◽  
And Migration ◽  
Relevant Variation ◽  
Novel Allele

The importance of interspecific introgression as a source of adaptive variation is increasingly recognized. Theory predicts that beneficial genetic variants cross species boundaries easily even when interspecific hybridization is rare and gene flow is strongly constrained throughout the genome. However, it remains unclear whether certain classes of genes are particularly prone to adaptive introgression. Genes affected by balancing selection (BS) may constitute such a class, because forms of BS that favour novel, initially rare alleles, should facilitate introgression. We tested this hypothesis in hybridizing newts by comparing 13 genes with signatures of BS, in particular an excess of common non-synonymous polymorphisms, to the genomic background (154 genes). Parapatric hybridizing taxa were less differentiated in BS candidate genes than more closely related allopatric lineages, while the opposite was observed in the control genes. Coalescent and forward simulations that explored neutral and BS scenarios under isolation and migration showed that processes other than differential gene flow are unlikely to account for this pattern. We conclude that BS, probably involving a form of novel allele advantage, promotes introgression. This mechanism may be a source of adaptively relevant variation in hybridizing species over prolonged periods.

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